Sequence
atgc intronic sequence ATGC exonic sequencegttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
---gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtcctt-----ggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
|| ||| | | | || ||| ||||| | || | | | || | | || || | | ||| || ||||||||| ||||||||||||||||||| ||||| || ||||||||||| || || ||||||||| | | | || || | ||||||||||| ||||| ||
taccttttttcttttctttt-tattcttatttctagcttatagttctcttctttctgtcacacacctaaaatggccattgttcttatt-ttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 2
gttagaacttgtgtactgcatacttttt--tcttagtagtatgt-taactatagtagtt-gtgtccttggtgtttata----ttcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
| || | | | | | |||| || | | || | || || || | || || | | || ||| | ||| | | |||||||| ||||||||||||||||||| |||||||| ||||||||| | ||||||||||||| ||| | | || || || |||||||| || ||||| ||
--aacgacgagaatgttaccttgttttgcacctgattggtgcctctacctgtactgctttgtatttcagaatttaataagaactacttgtgtatctgtgtagAAATTTGAGGGAGATGTTCAAGATTGATGCAGCGGATTATATGGTTTCCATTTGTGGAAGTGACGCACTTAGGGAGCTATCTTCTCCTGGAAAGAGTGGA
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------gttagaacttgtgtactgcatacttttttcttagtagt-----atgttaactatagtagt---tgtgtccttggtg-------tttatattcattgctaaacc----ttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
|| | || | | |||| | |||| | || | || |||| || | | ||| | ||| || | | || | | | || |||||| || |||| |||||||||||||| ||||| || || |||||||| ||||| ||||||||| | || | || |||| ||||| || || ||||| ||
gtccgcatttcttaaaaaaatatggtcttatccactgcaaattgagtgacatttagattgtacagaattttgttcattgggacctcttgttgacatattctttttgttgtttctcctggcttaaaatatactattctttctgttcctggctcaatactttaaaacacaatattgatccacttttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGTGGAAATTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
-gttag-aacttgtgt-actgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattca---ttgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
|| || |||| ||| || | |||||||| | | | || | | | | | || | |||||| ||| | ||| ||||| |||| ||| |||||||||| ||||| ||||| ||||||||||||||||||||||||||| || | || |||||||||||||||||||| || ||
agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
------gttagaacttgtg--tactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
|| || | | ||| || ||||||| | | | | || | | | ||| ||| ||| ||| | ||| | ||| ||||| |||| ||| |||||||||| ||||| ||||| ||||||||||||||||||||||| ||| || | || |||||||||||||||||||| || ||
tacatagtaaggaaccattgttacagccccctttttttcttctc-tcttttcctttcactttgcatgtgattgttgtatatgacc-ttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
-------gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaacct--tgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
| | ||| ||| || | ||| |||| | | || | | | | | ||| | |||| | | | |||| || ||||| |||| ||| |||||||||| ||||| || ||||| |||||||||||||||||||| |||||| | || ||||| |||||||| ||||| || ||
tgttcttatagacaactgt-tacagctcatctttctcttctc--tttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
-----------gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
| || || | | | || |||| | | || | | | | || | | | | || | | | | | || ||| || || | ||||||||||| ||||| ||||| ||||| || |||||||||||||| ||||||||| || | || |||||||||||||| ||||| || ||
tgtcttgatttaccaaaatttatagaat---taaattttgttaattaatgtacttaagat-gcacacct-ttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ34272 (Selaginella moellendorffii), 3'ss of exon 2
gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtt---tatattcattgctaaaccttgt-agAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
|| || | | || || | || | | | | | || ||| | | || | | || | | ||| || |||| || ||| | ||||| |||||||| |||||||||||| | || |||||||||| ||| || | |||||||||||||||| || ||||| |||
------------gtcctacttttccttagctcttccg-atttcccatttggcatttcatcttttgacgctctgtacagttttttttgttgcatgtcagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGC
upper sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 2
gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtt---tatattcattgctaaaccttgt-agAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
|| || | | || || | | || | | | | | || ||| | | || | | || | | ||| || |||| || ||| | ||||| |||||||| |||||||||||| | || |||||||||| ||| || | |||||||||||||||| || ||||| |||
------------gtcctacttttccttagctctttcg-atttcccatttggcatttcatcttttgacgctctgtacagttttttttgttgcatgtcagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttaactatagtagttgtgtccttggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
tgctaaa putative branch site (score: 2)
tgtttatattcatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA